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Enable users to simultaneously search all SearchBasedFetchers #6504
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koppor
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JabRef:master
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DominikVoigt:feature/add-option-to-fetch-from-all-sources
May 27, 2020
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703d000
Add CompositeSearchBasedFetcher to offer the option to query all libr…
DominikVoigt 3045da1
Add Test for CompositeSearchBasedFetcher.
DominikVoigt c6838a5
Reformat stream to increase readability.
DominikVoigt 81c4d81
Add CHANGELOG entry under Added.
DominikVoigt a6cf33a
Add Linebreak to CHANGELOG.
DominikVoigt abf4701
Add Linebreak to CompositeSearchBasedFetcherTest to fix checkstyle is…
DominikVoigt 51ec020
Update CHANGELOG.md
DominikVoigt 55ac9be
Add parameterized tests for CompositeSearchBasedFetcher.
DominikVoigt c3c0b65
Add better parameterized test naming.
DominikVoigt 7fa24e4
Implement requested change.
DominikVoigt 1947b1f
Merge branch 'feature/add-option-to-fetch-from-all-sources' of https:…
DominikVoigt 836fc31
Merge branch 'master' into feature/add-option-to-fetch-from-all-sources
DominikVoigt 1acd5aa
Remove GrobidCitationFetcher from test set as it was removed from set…
DominikVoigt da09f97
Add null check for CompositeSearchBasedFetcher.
DominikVoigt f07fa33
Modify Stream of Arguments according to recommendation.
DominikVoigt 2c70b3f
Change size of inkrement from 3 to 273 due to too many test arguments…
DominikVoigt 7d2b006
Merge branch 'master' into feature/add-option-to-fetch-from-all-sources
DominikVoigt 5f446c1
Reformat steam operators.
DominikVoigt d9454c5
Merge branch 'master' into feature/add-option-to-fetch-from-all-sources
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57 changes: 57 additions & 0 deletions
57
src/main/java/org/jabref/logic/importer/fetcher/CompositeSearchBasedFetcher.java
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package org.jabref.logic.importer.fetcher; | ||
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import java.util.List; | ||
import java.util.Optional; | ||
import java.util.Set; | ||
import java.util.stream.Collectors; | ||
import java.util.stream.Stream; | ||
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import org.jabref.logic.help.HelpFile; | ||
import org.jabref.logic.importer.FetcherException; | ||
import org.jabref.logic.importer.SearchBasedFetcher; | ||
import org.jabref.model.entry.BibEntry; | ||
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import org.slf4j.Logger; | ||
import org.slf4j.LoggerFactory; | ||
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public class CompositeSearchBasedFetcher implements SearchBasedFetcher { | ||
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private static final Logger LOGGER = LoggerFactory.getLogger(CompositeSearchBasedFetcher.class); | ||
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private final Set<SearchBasedFetcher> fetchers; | ||
private final int maximumNumberOfReturnedResults; | ||
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public CompositeSearchBasedFetcher(Set<SearchBasedFetcher> searchBasedFetchers, int maximumNumberOfReturnedResults) | ||
throws IllegalArgumentException { | ||
if (searchBasedFetchers == null) { | ||
throw new IllegalArgumentException("The set of searchBasedFetchers must not be null!"); | ||
} | ||
// Remove the Composite Fetcher instance from its own fetcher set to prevent a StackOverflow | ||
this.fetchers = searchBasedFetchers.stream() | ||
.filter(searchBasedFetcher -> searchBasedFetcher != this) | ||
.collect(Collectors.toSet()); | ||
this.maximumNumberOfReturnedResults = maximumNumberOfReturnedResults; | ||
} | ||
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@Override | ||
public List<BibEntry> performSearch(String query) { | ||
return fetchers.stream().flatMap(searchBasedFetcher -> { | ||
try { | ||
return searchBasedFetcher.performSearch(query).stream(); | ||
} catch (FetcherException e) { | ||
LOGGER.warn(String.format("%s API request failed", searchBasedFetcher.getName()), e); | ||
return Stream.empty(); | ||
} | ||
}).parallel().limit(maximumNumberOfReturnedResults).collect(Collectors.toList()); | ||
} | ||
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@Override | ||
public String getName() { | ||
return "SearchAll"; | ||
} | ||
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@Override | ||
public Optional<HelpFile> getHelpPage() { | ||
return Optional.empty(); | ||
} | ||
} |
125 changes: 125 additions & 0 deletions
125
src/test/java/org/jabref/logic/importer/fetcher/CompositeSearchBasedFetcherTest.java
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package org.jabref.logic.importer.fetcher; | ||
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import java.util.ArrayList; | ||
import java.util.Collections; | ||
import java.util.HashSet; | ||
import java.util.List; | ||
import java.util.Set; | ||
import java.util.stream.Stream; | ||
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import org.jabref.logic.bibtex.FieldContentFormatterPreferences; | ||
import org.jabref.logic.importer.FetcherException; | ||
import org.jabref.logic.importer.ImportFormatPreferences; | ||
import org.jabref.logic.importer.SearchBasedFetcher; | ||
import org.jabref.model.entry.BibEntry; | ||
import org.jabref.testutils.category.FetcherTest; | ||
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import org.junit.jupiter.api.Assertions; | ||
import org.junit.jupiter.api.Test; | ||
import org.junit.jupiter.params.ParameterizedTest; | ||
import org.junit.jupiter.params.provider.Arguments; | ||
import org.junit.jupiter.params.provider.MethodSource; | ||
import org.slf4j.Logger; | ||
import org.slf4j.LoggerFactory; | ||
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import static org.mockito.Mockito.mock; | ||
import static org.mockito.Mockito.when; | ||
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@FetcherTest | ||
public class CompositeSearchBasedFetcherTest { | ||
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private static final Logger LOGGER = LoggerFactory.getLogger(CompositeSearchBasedFetcherTest.class); | ||
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@Test | ||
public void createCompositeFetcherWithNullSet() { | ||
Assertions.assertThrows(IllegalArgumentException.class, | ||
() -> new CompositeSearchBasedFetcher(null, 0)); | ||
} | ||
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@Test | ||
public void performSearchWithoutFetchers() { | ||
Set<SearchBasedFetcher> empty = new HashSet<>(); | ||
CompositeSearchBasedFetcher fetcher = new CompositeSearchBasedFetcher(empty, Integer.MAX_VALUE); | ||
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List<BibEntry> result = fetcher.performSearch("quantum"); | ||
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Assertions.assertEquals(result, Collections.EMPTY_LIST); | ||
} | ||
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@ParameterizedTest(name = "Perform Search on empty query.") | ||
@MethodSource("performSearchParameters") | ||
public void performSearchOnEmptyQuery(Set<SearchBasedFetcher> fetchers) { | ||
CompositeSearchBasedFetcher compositeFetcher = new CompositeSearchBasedFetcher(fetchers, Integer.MAX_VALUE); | ||
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List<BibEntry> queryResult = compositeFetcher.performSearch(""); | ||
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Assertions.assertEquals(queryResult, Collections.EMPTY_LIST); | ||
} | ||
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@ParameterizedTest(name = "Perform search on query \"quantum\". Using the CompositeFetcher of the following " + | ||
"Fetchers: {arguments}") | ||
@MethodSource("performSearchParameters") | ||
public void performSearchOnNonEmptyQuery(Set<SearchBasedFetcher> fetchers) { | ||
CompositeSearchBasedFetcher compositeFetcher = new CompositeSearchBasedFetcher(fetchers, Integer.MAX_VALUE); | ||
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List<BibEntry> compositeResult = compositeFetcher.performSearch("quantum"); | ||
for (SearchBasedFetcher fetcher : fetchers) { | ||
try { | ||
Assertions.assertTrue(compositeResult.containsAll(fetcher.performSearch("quantum"))); | ||
} catch (FetcherException e) { | ||
/* We catch the Fetcher exception here, since the failing fetcher also fails in the CompositeFetcher | ||
* and just leads to no additional results in the returned list. Therefore the test should not fail | ||
* due to the fetcher exception | ||
*/ | ||
LOGGER.debug(String.format("Fetcher %s failed ", fetcher.getName()), e); | ||
} | ||
} | ||
} | ||
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/** | ||
* This method provides other methods with different sized sets of search-based fetchers wrapped in arguments. | ||
* | ||
* @return A stream of Arguments wrapping set of fetchers. | ||
*/ | ||
static Stream<Arguments> performSearchParameters() { | ||
ImportFormatPreferences importFormatPreferences = mock(ImportFormatPreferences.class); | ||
when(importFormatPreferences.getFieldContentFormatterPreferences()) | ||
.thenReturn(mock(FieldContentFormatterPreferences.class)); | ||
List<Set<SearchBasedFetcher>> fetcherParameters = new ArrayList<>(); | ||
List<SearchBasedFetcher> list = new ArrayList<>(); | ||
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list.add(new ArXiv(importFormatPreferences)); | ||
list.add(new INSPIREFetcher(importFormatPreferences)); | ||
list.add(new GvkFetcher()); | ||
list.add(new AstrophysicsDataSystem(importFormatPreferences)); | ||
list.add(new MathSciNet(importFormatPreferences)); | ||
list.add(new ZbMATH(importFormatPreferences)); | ||
list.add(new GoogleScholar(importFormatPreferences)); | ||
list.add(new DBLPFetcher(importFormatPreferences)); | ||
list.add(new SpringerFetcher()); | ||
list.add(new CrossRef()); | ||
list.add(new CiteSeer()); | ||
list.add(new DOAJFetcher(importFormatPreferences)); | ||
list.add(new IEEE(importFormatPreferences)); | ||
/* Disabled due to an issue regarding comparison: Title fields of the entries that otherwise are equivalent differ | ||
* due to different JAXBElements. | ||
*/ | ||
// list.add(new MedlineFetcher()); | ||
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// Create different sized sets of fetchers to use in the composite fetcher. | ||
// Selected 273 to have differencing sets | ||
for (int i = 1; i < Math.pow(2, list.size()); i += 273) { | ||
Set<SearchBasedFetcher> fetchers = new HashSet<>(); | ||
// Only shift i at maximum to its MSB to the right | ||
for (int j = 0; Math.pow(2, j) <= i; j++) { | ||
// Add fetcher j to the list if the j-th bit of i is 1 | ||
if ((i >> j) % 2 == 1) { | ||
fetchers.add(list.get(j)); | ||
} | ||
} | ||
fetcherParameters.add(fetchers); | ||
} | ||
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return fetcherParameters.stream().map(Arguments::of); | ||
} | ||
} |
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Can you provide me the concreete example? Maybe, we need to fix the MedlineFetcher?
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AFAIK:
When using the same instance of MedlineFetcher to fetch results directly or as part of the CompositeFetcher, certain BibEntries have differing titles due to something related to JAXBElements.
When searching for "Indistinguishable Photons from Deterministically" the direct use of the MedLine Fetcher returns a BibEntry with the title:
The CompositeFetcher, on the other hand, returns a BibEntry with the title:
Both would be the same only differing by the JAXBElement Instance.